Many of major autoimmune diseases are sexually dimorphic. Systemic Lupus Erythematosus (SLE), scleroderma, multiple sclerosis, Sjogren's syndrome, and some forms of Type 1 diabetes (T1D) are primarily occurring in females. It has been attributed to multiple factors including expression of the genes encoded by sex chromosomes, hormonal regulation of gene expression, and lately to unexpected regulation by commensal microbiota. Thus, understanding of sexual dimorphism of diseases requires that the problem be approached by a combination of different strategies. In this proposal, we take advantage of our abilities to perform state of the art experiments using genetically modified and gnotobiotic animals with original and constantly developing computational methods. Our preliminary data demonstrates the efficiency of such an integrative approach to the problem. We have suggested a `dual signal' model of autoimmunity involving regulation by microbes and sex hormones. Accordingly, hormonal and microbial influences do not have to be simultaneous: they may be important at different stages of development or disease progression. We already identified a number of genes that are regulated by hormone (androgen) receptors and are now posed to elucidate the connection between such regulation and autoimmunity. Given the complexity of the problem, we plan to pursue several carefully selected goals that will lay foundation for the future expansion of research in this important area. Aim 1: Test the dual signal model of microbial involvement in sexual dimorphism of autoimmunity. We will test whether gene expression patterns and chromatin status in T cells and macrophages are regulated by hormones independently of the microbiota. Aim 2: Elucidate specific mechanisms involved in hormonal regulation of immunity We will study the mechanisms of hormone and microbe-dependent regulation of IFN? production: we will test the hypothesis that a long non-coding RNA termed NeST controls the gender bias of IFN? production, and test its relevance to the gender bias in Type 1 Diabetes (T1D). We will study the role of sex hormones in contribution to expression of regulatory phosphatase Ptpn22 and its role in T1D. Aim 3: The role of microbiota in sexual dimorphism of systemic autoimmunity To determine how general the role of microbiota is in sexual dimorphism, we will test a model of systemic autoimmunity with well-established sexual dimorphism -B6.NZM mice- in SPF and GF conditions. We will determine a role of model genes regulated by androgens (NeST and Ptpn22) we will manipulate hormone-responsive elements in their promoters and test the consequences in Systemic Lupus Erythematosus (SLE).